moving to v0.6.1

Author: trtcrd

Dockerfile

@@ -59,8 +59,10 @@ RUN R -e 'install.packages("dplyr", repos="https://stat.ethz.ch/CRAN/")'
 RUN R -e 'install.packages("seqinr", repos="https://stat.ethz.ch/CRAN/")'
 RUN R -e 'library(devtools);install_github("tobiasgf/lulu")'
 RUN R -e 'install.packages("BiocManager",dependencies=TRUE,repos="https://stat.ethz.ch/CRAN/")'
-RUN R -e 'BiocManager::install("DECIPHER")'
-RUN R -e 'BiocManager::install("dada2")'
+#RUN R -e 'BiocManager::install("DECIPHER")'
+#RUN R -e 'BiocManager::install("dada2")'
+RUN R -e 'library(devtools);devtools::install_github("benjjneb/dada2", ref="v1.16")'
+RUN R -e 'install.packages("https://www.bioconductor.org/packages/3.11/bioc/src/contrib/Archive/DECIPHER/DECIPHER_2.16.0.tar.gz", repos = NULL, type = "source")'
 
 
 # ----- Libraries deployments -----

README.md

@@ -12,7 +12,7 @@ See below for full instructions
 
 # Accessing the webserver
 
-The execution of the `start_slim_v0.6.sh` script deploys and start the webserver.
+The execution of the `start_slim_v0.6.1.sh` script deploys and start the webserver.
 By default, the webserver is accessible on the 8080 port.
 
 * To access it on a remote server from your machine, type the server IP address followed by ":8080" (for example `156.241.0.12:8080`) from an internet browser (prefer Firefox and Google Chrome).
@@ -149,12 +149,12 @@ First of all, docker needs to be installed on the machine. You can find instruct
 * [docker for Ubuntu](https://docs.docker.com/install/linux/docker-ce/ubuntu/)
 * [docker for macOS](https://docs.docker.com/docker-for-mac/install/)
 
-To install SLIM, get the last stable release [here](https://github.com/trtcrd/SLIM/archive/v0.6.tar.gz) or, using terminal :
+To install SLIM, get the last stable release [here](https://github.com/trtcrd/SLIM/archive/v0.6.1.tar.gz) or, using terminal :
 ```bash
 sudo apt-get update && apt-get install git curl
-curl -OL https://github.com/trtcrd/SLIM/archive/v0.6.tar.gz
-tar -xzvf v0.6.tar.gz
-cd SLIM-0.6
+curl -OL https://github.com/trtcrd/SLIM/archive/v0.6.1.tar.gz
+tar -xzvf v0.6.1.tar.gz
+cd SLIM-0.6.1
 ```
 
 Before deploying SLIM, you need to configure the mailing account that will be used for mailing service.
@@ -174,13 +174,13 @@ exports.mailer = {
 ```
 
 
-As soon as docker is installed and running, the SLIM archive downloaded and the mailing account set, it can be deployed by using the two scripts `get_dependencies_slim_v0.6.sh` and `start_slim_v0.6.sh` as **super user**.
-* `get_dependencies_slim_v0.6.sh` fetches all the bioinformatics tools needed from their respective repositories.
-* `start_slim_v0.6.sh` destroys the current running webserver to replace it with a new one. **/!\\** All the files previously uploaded and the results of analysis will be detroyed during the process.
+As soon as docker is installed and running, the SLIM archive downloaded and the mailing account set, it can be deployed by using the two scripts `get_dependencies_slim_v0.6.1.sh` and `start_slim_v0.6.1.sh` as **super user**.
+* `get_dependencies_slim_v0.6.1.sh` fetches all the bioinformatics tools needed from their respective repositories.
+* `start_slim_v0.6.1.sh` destroys the current running webserver to replace it with a new one. **/!\\** All the files previously uploaded and the results of analysis will be detroyed during the process.
 
 ```bash
-sudo bash get_dependencies_slim_v0.6.sh
-sudo bash start_slim_v0.6.sh
+sudo bash get_dependencies_slim_v0.6.1.sh
+sudo bash start_slim_v0.6.1.sh
 ```
 
 The server is configured to use up to 8 CPU cores per job. The amount of available cores will determine the amount of job that can be executed in parallel (1-8 -> 1 job, 16 -> 2 jobs, etc.). To admin and access SLIM logs, please refer to the docker command line [documentation](https://docs.docker.com/engine/reference/commandline/docker/).
@@ -219,9 +219,13 @@ Please refer to the wiki pages to learn [how to create a module](https://github.
 
 # Version history
 
+### v0.6.1
+
+Dockerfile: updated to DADA2 v1.16 and DECIPHER v2.16.0, cleaned the docker recipe
+
 ### v0.6
 
-BUGFIX: resolved issues with the order of module execution when DADA2 is used. 
+BUGFIX: resolved issues with the order of module execution when DADA2 is used.
 BUGFIX: resolved issues with the pipeline.conf file that did not included the checkbox and radio buttons.
 
 ### v0.5.3